snATACseq analysis with ArchR - GE cluster QC 1.

Results

Cluster QC

No Harmony

Cluster that expresses SPI1 and SLC17A7 to remove: C7

  • Cell count before filter = 6430
  • Cell count after filter = 6006

Remove clusters that do not have >= 30 cells in at least 2 donors:

  • Cell count before filter = 6006
  • Clusters to be retained from initial QC pass = C10, C9, C8, C1, C2, C11, C5, C4, C3
  • No. of cells to be removed = 157
  • Cell count after filter = 5849
Reclustering plots

Batch corrected cell counts per cluster

C1 C10 C2 C3 C4 C5 C6 C7 C8 C9
215 1130 178 481 922 738 656 579 531 434
UMAPs

Unconstrained Integration

Cluster mappings

RNA InN-1 RG-1 InN-6 InN-7 CycPro InN-3 RG-3 RG-2 RG-3 InN-1
ATAC C5 C7 C9 C1 C8 C4 C2 C10 C3 C6

Cell counts

UMAP

With Harmony

Cluster that expresses SPI1 and SLC17A7 to remove: C11

  • Cell count before filter = 6006
  • Cell count after filter = 5996

Remove clusters that do not have >= 30 cells in at least 2 donors:

  • Cell count before filter = 5996
  • Clusters to be retained from initial QC pass = C6, C3, C12, C1, C8, C2, C7, C4, C9
  • No. of cells to be removed = 132
  • Cell count after filter = 5864
Reclustering plots

UMAPs

Unconstrained Integration

Cluster mappings

RNA InN-1 RG-1 InN-6 InN-7 InN-3 RG-3 RG-2 InN-1 InN-1
ATAC C8 C3 C5 C1 C7 C2 C4 C6 C9

Cell counts

UMAP